Catch-up Dec 9th – April 30th

I will cover coronavirus separately. In the meantime, a lot has been happening in genomics more broadly. I’ll draw your attention to:

  1. Ongoing controversy about Precision Medicine. Two pieces question the prominence it receives Precision medicine: course correction urgently needed and Promises and perils of using genetic tests to predict risk of disease. Meanwhile The Personalized Medicine Coalition has helped put together a new bipartisan caucus to advance support for personalized medicine in Washington.
  2. A host of new common disease/complex trait work (separated into its own section below), including GWAS for self-reported childhood maltreatment, income, alcohol intake, lifespan. A few papers that have looked at including polygenic scores in clinical models, with mixed results.
  3. A remarkable amount of legislative efforts, including a Bill on the Governor of Florida’s desk that would close some GINA loopholes, and efforts in Utah, New Jersey, and California
  4. DNA from detained immigrants is being added to the federal national DNA database, CODIS, which was originally established to track violent federal offenders

 

Science

  • From October, prime-editing, akin to “search and replace” rather than “cut and paste”, which doesn’t require a double strand break “Prime editing substantially expands the scope and capabilities of genome editing, and in principle could correct up to 89% of known genetic variants associated with human diseases.” In the first few weeks post the publication of this article the researchers were inundated with requests for constructs.
  • Some updates from All Of Us: 339,000 consented participants, 265,000 completed the full protocol, 50% from racial and ethnic minorities, 80% from populations underserved in biomedical research. “This is more than just a data resource. It’s an ecosystem” that includes data analysis tools and participant outreach.
  • Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, reporting on the matched tumor-normal sequencing of 2,658 individuals. Key findings included: average of 4-5 driver mutations per cancer; only 5% tumors lacked any identified driver mutation; large rates of  chromoplexy (17.8% of tumours) and chromothripsis (22.3%); change of mutational signature over time in 40% of tumors; driver mutations can occur years before cancer diagnosis. 
  • The NHGRI have published their draft Genomics 2020 strategic plan. They invite comments.
  • Anti-CRISPRs exist in the wild, as part of the viral counter-attack to the bacterial counter-attack that is the main function of CRISPR systems in bacteria. There are also several other attempts to produce a “stop button” for gene editing, which should have as a by-product editing which can be better targeted to particular cell types and to reduce off-(sequence)-target effects. (Link to an easy to read nature news feature summary).

 

Polygenics: Common diseases/complex traits

 

Applications

 

Regulation etc